Alternate City of Glass
by lcelinaoc
Summary: AU during CoG. After Jace yells at Clary and tells her to go home, instead of disobeying, Clary actually returns to NY. But when she returns home, someone is waiting for her, and it's up to Jace to save her. That is, if he still wants to.
1. Chapter 1

Alternate City of Glass

**A/N: Okay, for those of you who have read my other story, this is only my second story, so you probably know I'm not the best author. Wow, I just realized how long it's going to take to put in the actual argument... Anyway, I think that's all I have to say for now. Oh, and whatever is in ****_italics _or whatever it's called, is directly from the book, give or take some grammatical errors : )**

**Summary: Clary just got yelled at by Jace (in CoG) and decided to do what he said and leave. But when she returns to NY, someone is waiting for her...**

**Disclaimer: I'm not Cassandra Clare, and, sadly, all of this belongs to her : ( Especially this entire chapter, not including my A/N's and Disclaimer**

_"Jace," she said, and took a step toward him._

_He backed away from her as if she were coated in something poisonous. "What," he said, "in the name of the Angel, Clary, are you doing here?"_

_Despite everything, the harshness of his tone hurt. "You could at least pretend you were glad to see me. Even a little bit."_

_"I'm not glad to see you," he said. Some of his color had come back, but the shadows under his eyes were still gray smudges against his skin. Clary waited for him to say something else, but he seemed content just to stare at her in undisguised horror. She noticed with a distracted clarity that he was wearing a black sweater that hung off his wrist as if he'd lost weight, and that the nails on his hands were bitten down to the quick. "Not even a little bit."_

_"This isn't you," she said. "I hate it when you act like this-"_

_"Oh, you hate it, do you? Well, I'd better stop doing it, then, hadn't I? I mean, you do everything _I _ask you to do."_

_"You had no right to do what you did!" she snapped at him, suddenly furious. "Lying to me like that. You had no right-"_

_"I had _every right_!" he shouted. She didn't think he'd ever shouted at her before. "I had every right, you stupid, stupid girl. I'm your brother and I-"_

_"And you what? You own me? You don't own me, whether you're my brother or not!"_

_The door behind Clary flew open. It was Alec, soberly dressed in a long, dark blue jacket, his black hair in disarray. He wore muddy boots and an incredulous expression on his usually calm face. "What in all possible dimensions is going on in here?" he said, looking from Jace to Clary with amazement. "Are you two trying to kill each other?"_

_"Not at all," said Jace. As if by magic, Clary saw, it had all been wiped away: his rage and his panic, and he was icy calm again. "Clary was just leaving."_

_"Good," Alec said, "Because I need to talk to you, Jace."_

_"Doesn't anyone in this house ever say, 'Hi, nice to see you' anymore" Clary demanded of no one in particular._

_It was much easier to guilt Alec than Isabelle. "It _is _good to see you, Clary," he said, "except of course for the fact that you're really not supposed to be here. Isabelle told me you got here on your own somehow, and I'm impressed-"_

_"Could you _not _encourage her?" Jace inquired._

_"But I really, really need to talk to Jace about something. Can you give us a few minutes?"_

_"I need to talk to him too," she said. "About our mother-"_

_"I don't feel like talking," said Jace, "to either of you, as a matter of fact."_

_"Yes you do," Alec said. "You really want to talk to me about this."_

_"I doubt that," Jace said. He had turned his gaze back to CLary. "You didn't come here alone, did you?" he said slowly, as if realizing that the situation was even worse than he'd thought. "Who came with you?"_

_There seemed to be no point in lying about it. "Luke," said Clary. "Luke came with me._

_Jace blanched. "But LUke is a Downworlder. Do you know what the Clave does to unregistered Downworlders who come into the Glass City-who cross the wards without permission? Coming into Idris is one thing, but entering Alicante? Without telling anyone?"_

_"No," Clary said, in a half whisper, "but I do know what you're going to say-"_

_"That if you and Luke don't go back to New York immediately, you'll find out?"_

_For a moment Jace was silent, meeting her eyes with his own. The desperation in his expression shocked her. He was the one threatening her, after all, not the other way around._

_"Jace," Alec said into the silence, a tinge of panic creeping into his voice. "Haven't you wondered where I've been all day?"_

_"That's a new coat you're wearing," Jace said, without looking at his friend. "I figure you went shopping. Though why you're so eager to bother me about it, I have no idea."_

_"I didn't go shopping," Alec said furiously. "I went-"_

_The door opened again. In a flutter of white dress, Isabelle darted in, shutting the door behind her. She looked at CLary and shook her head. "I told you he'd freak out," she said. "Didn't I?"_

_"Ah, the 'I told you so,'" Jace said. "Always a classy move."_

_Clary looked at him with horror. "How can you _joke_?" she whispered. "You just threatened Luke. Luke, who likes you and trusts you. Because he's a _Downworlder. _What's wrong with you?"_

_Isabelle looked horrified. "Luke's here? Oh, Clary-"_

_"He's _not_ here," Clary said. "He left-this morning-and I don't know where he went. But I can certainly see now why he had to go." She could hardly bear to look at Jace. "Fine. You win. We should never have come. I should never have made that Portal-"_

_"_Made_ a Portal?" Isabelle looked bewildered. "Clary, only a warlock can make a Portal. And there aren't very many of them. The only Portal here in Idris in the Gard."_

_Which is what I had to talk to you about," Alec hissed at Jace-who looked, Clary saw with surprise, even worse than he did before; he looked as if her were about to pass out. "About the errand I went on last night-the thing I had to deliver to the Gard-"_

_"Alec, stop. _Stop,_" Jace said, and the harsh desperation in his voice cut the other boy off; Alec shut his mouth and stood staring at Jace, his lip caught between his teeth. But Jace didn't seem to see him; he was looking at Clary and his eyes were hard as glass. Finally he spoke. "You're right," he said in a choked voice, as if he had to force out the words. "You should never have come. I know I told you it's because it isn't safe for you here, but that wasn't true. The truth is that I don't want you here because you're rash and thoughtless and you'll mess everything up. It's just how you are. You're not careful, Clary."_

_"Mess...everything...up?" Clary couldn't get enough air into her lungs for anything but a whisper._

_"Oh, _Jace,_" Isabelle said sadly, as if _he_ were the one__ who was hurt. He didn't look at her. His gaze was fixed on Clary._

_"You always just race ahead without thinking," he said. "You know that, Clary. We'd never have ended up in the Dumort if it wasn't for you."_

_"And Simon would be _dead!_ Doesn't that count for anything? Maybe it was rash, but-"_

_His voice rose, "_Maybe_?_"

_"But it's not like every decision I've made was a bad one! You said, after what I did on the boat, you said I'd saved everyone's life-"_

_All the remaining color in Jace's face went. He said, with a sudden and astounding viciousness, "Shut up, Clary. SHUT UP-"_

_"On the boat?" Alec's gaze danced between them, bewildered. "What about what happened on the boat? Jace-"_

_"I just told you that to keep you from whining!" Jace shouted, ignoring Alec, ignoring everything but Clary. She could feel the force of his sudden anger like a wave threatening to knock her off her feet. "You're a disaster for us, Clary! You're a mundane, you'll always be one, you'll never be a Shadowhunter. You don't know how to think like we do, think about what's best for everyone-all you ever think about is yourself! But there's a war on now, or there will be, and I don't have the time or the inclination to follow around after you, trying to make sure you don't get one of us killed!"_

_She just stared at him. She couldn't think of a thing to say; he'd never spoken to her like this. She'd never even imagined him speaking to her like this. However angry she'd managed to make him in the past, he'd never spoken to her as if he hated her before._

_"Go home, Clary," he said._

**A/N: Okay, I know there's more to the argument, but I think that'll work. And I'm sorry there's no page number, but I bought the book on my Amazon Kindle, and that doesn't have page numbers, it has 'locations.' For example, this is on 1827. I'm pretty sure that the book is not almost 2000 pages. I meant to make the chapter longer with some of my own stuff, but that seemed enough, for now, so it'll be in the next chapter. Anyway, what do you think? R & R, please : )**


	2. Chapter 2

Chapter 2

**A/N: Okay, here's the second chapter to my newest story. This one will definitely be in my own words, not completely copied from the book ; ) Wow, I just noticed it's 3:06 a.m. and I'm supposed to be up in 54 minutes so I can go on vacation. Oh, well, I'll sleep in the car. This is more fun, anyway.**

**Disclaimer: I'm Cassandra Clare. Wait, no I'm not :'O**

_"Go home, Clary."_ The words that kept repeating themselves over, and over, and over again in her mind.

Clary was staring at Amatis's wall. If she concentrated hard enough, she could almost see the words that had haunted her mind for hours on end engraved into the wall. _It's over,_ she thought. _Jace doesn't want me around. He's right, too, I do mess everything up. I'm a mundane that's acting like a shadowhunter._

Clary spoke out loud, "Well if he doesn't want me here, then I'll leave." She walked over to the trunk Amatis had left for her. It was filled with Shadowhunter clothing, a wedding dress, what looked like school clothes, and a silver dress. Clary sighed and took off the black Shadowhunter gear she was wearing and put on the plaid skirt and a white button up shirt. "At least I'll look like I go to a private school when I get back to New York, and not some weirdo," Clary muttered to herself. Giving one last, sad glance at the Shadowhunter gear, she closed the lid of the trunk.

Quietly, she made her way down the stairs and into the kitchen. From there, she saw several doors leading off. She'd come from one, the other was the living room, one was a hallway, and the fourth...

She opened it and grinned. It lead to some descending stairs that led into a very open room. Clary knew that this was the training room of the house and where the training room was, the weapons were sure to be. After admiring the room for a few minutes, Clary noticed a door leading off of the training room. When she opened the door, she was pleased to find a room full of seraph blades, steles, kindjals, and more. She walked over to the small selection of steles and examined them. There was an old style one that reminded Clary of her mother's lost stele. As she reached for it, she hesitated. It was Amatis's stele, not hers. What if Amatis still used the stele? After hesitating a few moments, she grabbed a newer looking one that was silver.

After several minutes of looking around the room, she quietly shut the training room door behind her and looked around the kitchen. She quickly grabbed a pencil and paper she found on the counter and scribbled a note to Amatis and Luke saying she was leaving for New York again. Taking one last look around the kitchen, she opened the kitchen door and left.

* * *

Jace stared at the wall. It had been hours since he had yelled at Clary. He leaned his head against the wall behind his bed as he remembered all the lies he'd fed to her while he yelled at her. He _never _lied to anyone. He _never _yelled at anyone like _that_, let alone his _sister/love_. He had watched Clary's destroyed face as he said those things, watched as she yelled back at him.

"It's not your fault," Jace looked up to see Alec leaning against the doorframe. "She came and she wasn't supposed to, that's that. You don't have to watch her-"

"Shut up," Jace cut him off.

Alec shrugged, "Dinner's ready, if you want some." With that, he left Jace to thinking.

After waiting another half hour, Jace snuck down the stairs and out the front door. Shoving his hands in his pockets, he walked down the street towards Amatis Herondale's house. After walking for a while, he reached her street. He paused a minute before he walked up the steps towards her house.

He knocked on the door. Slowly, he heard footsteps approaching the door, then yelling, "Clary! Why did you ever-" she broke off once she saw Jace.

"Oh, I'm sorry, I thought it was... never mind. How can I help you?" Amatis asked. Jace knew something was wrong. He knew it as soon as he heard Amatis yelling, thinking it was Clary.

"I'm Jace, is Clary here?" he asked.

Amatis blanched, "Um, no, she's not, actually. I thought you knew?"

Now Jace was really worried, "Knew what?"

"Knew that Clary left, for New York. Wait here, a minute." She left Jace in shock as he stared at the place where Amatis had been.

_She _left?_ How could she leave? _he thought to himself. Then with self loathing_, You told her to, remember?_

He was snapped out of his thoughts when he heard the click of Amatis's shoes on the wood floor as she returned.

"She left this, on her bed, for you." Amatis held out a letter for Jace to take.

He hesitated for a minute before taking it and saying, "Thank you."

Amatis nodded, slightly uncomfortable. Jace looked up and nodded before turning and walking down the steps that led up to her porch. He sat at the curb and took the letter out of the envolope.

_Jace, _it read,

_You're right, I screwed everything up. So, I've decided to go back to New York, like you wanted. I've decided to leave Shadowhunting behind, you're right, again, it's not for me. You were always right. I'm sorry._

_Clary_

**A/N: I'm cruel, I know. I think that's all I can write. It's now 3:50 and I have ten minutes before I'm supposed to wake up. Oh, well, hope you liked it! R & R! : )**


	3. Chapter 3

Chapter 3

**A/N: I'm so sorry I haven't updated in a while. During vacation, I'm usually really lazy! So, sorry. OMG! You are all such awesome reviewers. With my other story, I named all of my reviewers because I only had a few at the time, but most of my email inbox was full of reviews, author alerts, story alerts, fav. stories, it was so awesome! Thank you all so much! Honestly, I didn't think I was that good of an author! And I'm so, so, so sorry that I left the last chapter with a cliffhanger, but I kind of had to. Once again, really sorry : (**

**_THERE'S A POLL FOR THIS STORY ON MY PROFILE, PLEASE PLEASE VOTE!_**

**Disclaimer: Nope, not Cassandra Clare : (**

Jace stared at the note for what felt like hours. How? How could she leave?

"Jace?" he looked up to see Alec and Isabelle walking down the street.

"Hi, Alec, Izzy."

Isabelle looked at him for a second, "What happened now?"

"Clary's gone," was all he said.

Isabelle gasped, "What?"

"She left."

"What do you mean 'she left?'" Alec demanded.

"I mean," Jace said, "she went back to New York."

"Well, that's a good thing," Alec said. "Right?"

Jace laughed harshly, "Yeah, it would be, if she hadn't left this." He held out the note to Isabelle. She grabbed it and read it, her eyes widening.

"Why?" she gasped.

"Because I yelled at her."

Alec spoke quietly, "But isn't this what you wanted?"

Jace paused for a minute before replying, "Yes. I guess it was."

"Then what's the problem?" asked Alec.

Jace didn't say anything. Isabelle finally said, "You need to come home, we're waiting for you before we start dinner. Mom sent us out because you didn't come back."

"Fine, I'll come," he stood up, "What's for dinner?"

Alec shrugged. "No idea. They just sent us out before we could eat. Whatever it was, it smelled really good."

Isabelle laughed and even Jace chuckled. "Alright, let's go."

The three of them walked down the street, back towards the Penhallow's house.

**A/N: Yeah, wasn't much of a chapter, wasn't very good either. : ( But, this is all I could do for Jace. Next chapter will be about Clary. Hopefully, it will be easier. Well, R & R : )**


	4. Chapter 4

Chapter 4

**A/N: I'm so sorry I haven't updated! I'm a terrible person : ( I know. Anyway, here is the next chapter in my story! Oh, and this chap. is about Clary!**

**_THE POLL IS NOW CLOSED!! RESULTS WERE CLARY DID WRITE THE NOTE TO JACE: 5 AND CLARY DID NOT: 2. I'M NOT SAYING WHOSE RIGHT, YOU'LL FIND OUT LATER_**

**Disclaimer: Nope, not Cassandra Clare : (**

Clary sighed as she looked at the looming structure of the Institute down the street. She wasn't sure if she should go back or not.

"Come on, Fray, grow up," she muttered to herself as she tore herself away from the Institute. She had nothing left there, so no one could track her. After she drew another portal rune, she stepped through it and landed by Luke's house. Bitterly, she remembered the first time she'd traveled to a portal to this exact same place. Jace had gone through after her which resulted in him landing on top of her. "No!" she whispered to herself, "Jace doesn't care, he never cared. He doesn't want you, you can't depend on him forever." Slowly, she walked up to Luke's door and opened it with the hidden key.

She entered her room and grabbed her green backpack and filled it with all her stuff. After she'd checked to make sure the house had nothing of hers left, she glanced around the house for the last time before she closed the door behind her.

* * *

Clary decided that the first place for her to go was Luke's farm. So, she made another portal and fell onto a soft patch of grass by the farm. She sat up and stretched her muscles which had begun to seize up from traveling through so many portals in one day. Closing her eyes, Clary could almost pretend she was here with her mother, Luke, and Simon like always and nothing had happened. No Jace, no Shadowhunters, no downworlders... But Clary knew it was not the truth, and there was no point fantasizing about "what ifs..."

"Well, well, well. If it isn't the famous Clarissa Morgenstern," a voice said from behind her. Clary whirled around to see a boy about her age, give or take a year, strolling casually up the hill. He had black hair and looked very familiar.

"Do I know you?" Clary said, frowning.

"Not really, no. Though you did meet me recently," the boy smiled a charming smile that managed to show all his teeth.

Clary blinked in confusion as her mind went in and out of focus. "Um, what's your name again?"

"Sebastian," he stuck his hand out. Then he added, "Verlac. Sebastian Verlac." Clary nodded and shook his hand.

"And, where did I meet you?"

"Idris, of course," he smiled again. Clary was too distracted to notice a slight pressure on her finger and something cool slip around it.

Clary shook her head, as though trying to clear it. Everything in front of her got fuzzy. She suddenly felt the thing on her finger, as it was now burning her. She looked down to see a ring. It was a Morgenstern ring, Clary guessed from the coat of arms on it. The only difference between Jace's ring and the one currently on her hand now was the fact that hers seemed to be made for a girl rather than a boy.

That was all Clary noticed before the burning on her finger turned white hot and she saw stars dancing in front of her eyes. She wasn't aware of herself sagging into Sebastian's arms. Nor was she aware of the portal trip.

The last thing she heard was, "Father will be so pleased..."

**A/N: Sorry 'bout the cliffhanger! It just seemed like a great way to end it. Anyway, I'm starting on the next chapter immediately and it will probably be up within the hour if my parents are still oblivious to what I do at 1 a.m, lol. R & R!**


	5. Chapter 5

Chapter 5

**A/N: Darn, I was caught : ( I had to go to sleep and by the time I woke up, I completely forgot my idea! So, so, soooo sorry! I was sick for a while, but I'm finally back! Happy Belated Holidays!!!**

**Disclaimer: Nope, not Cassandra Clare : (**

Jace had been pacing his room angrily for the past hour. He knew it was impossible, but he had this nagging feeling that Clary was hurt and needed his help. No matter how hard he tried, he couldn't shake the feeling. Aline tried distracting him, but he pushed her away, more disgusted with himself than her. After several failed attempts by Alec and Isabelle, he was left in the confinements of his and Alec's room.

Almost half an hour later, Jace stormed out of the house saying he'd be back later and walked in a random direction. After walking for almost another half hour, Jace found himself facing the demon towers from a high hill and the country beyond that. Bitterly, he wished he had been able to show Clary around Alicante and all the beautiful places in Idris so she could draw and paint for hours. Sighing, he got up and turned back for the long walk it would take before he reached the Penhallow's house.

Something moved in the corner of his eye and he turned again. He realized he wasn't carrying a weapon and swore under his breath. Then, Sebastian walked out of the shadows. "Hello, Jace."

Jace narrowed his eyes at the boy. He hadn't seen Sebastian leave the Penhallow's, but then again, he hadn't really seen anybody while he was locked up in his room. Although, something still screamed "DANGER" and Jace's natural instinct to protect kicked in. Then Jace thought, protect what? No one was here with him with the exception of Sebastian and there was nothing valuable of his on this mountain.

"What do you want, Sebastian?" spat Jace.

Sebastian looked concerned, "What's up, dude? You seem worried."

_Dude?_ thought Jace. Shaking it off, he snorted, "What was your first guess?"

Sebastian shrugged, "Don't know. You've been sulking ever since your _sister_ left." Jace didn't miss how Sebastian pointed out 'sister.'

Jace glared at Sebastian and stood up and brushed off his pants. He walked by Sebastian without looking back. Slowly, he made his way back to the Penhallow's with his hands in his pockets and head held down. Even now, he felt the nagging sense that Clary needed him.

**A/N: I know, I know, it's wayyy toooo short after such a long break : ( But this is all I have for Jace (for now). I'm working on a Clary chapter next and hopefully it will be up soon, but I'm bad at keeping promises, so I'm not going to say one. R & R!**


	6. Chapter 6

Chapter 6

**A/N: I would say I have an awesome excuse for not updating in over a month (or has it been two...?), but, sadly, I've got nothing : ( I'm just a lazy person with terrible writers block! So, really sorry and sorry if some of you've given up on my stories! I'll try to update more, but no promises :(**

**Disclaimer: Don't own MI, all rights to Cassandra Clare.**

Clary was disoriented as she woke up. Blinking a few times, she opened her eyes. Propping herself on her elbows, she observed the room. It was more of a hallway filled with beds. Like a hospital. The walls, floors, ceiling, and just about everything else was white. The only splash of color was a painting above a white desk at the end of the hall. It was a picture of the ocean. Suddenly, she heard voices and she shoved her face back into the pillow and pretended to be asleep.

The doors crashed open and Clary jumped up. Looking next to the desk, she noted the two doors and three people coming through them. One, she recognized, was the boy from Luke's farm. Sebastian Verlac. The second was Valentine. Finally, a woman dressed in all white (like a nurse) followed looking very disapproving.

"Ah, Clarissa, you're awake," Valentine said as he stopped at the foot of her bed. Sebastian hung back a few steps.

The nurse, however, stepped forward, "Leave her alone, she needs rest! It's bad enough that you burned her, but then you had to drop her! She's not a heavy girl, and a shadowhunter should easily be able to support her weight." The nurse glared at Sebastian.

Sebastian shrugged and ignored her.

"Well, well, well. What to do," muttered Valentine.

He nodded to the nurse and she sighed. She turned back to Clary with an apologetic smile and reached into the pocket of her uniform. She pulled out an IV and hooked it up to the machine next to Clary's bed. Clary flinched away as the nurse moved towards her, but the nurse grabbed her arm and found the vein before pushing the needle in. Clary winced and closed her eyes.

The nurse checked something on the bag and machine before pulling part of the needle back out. Suddenly, Clary felt tired and could feel her eyelids drooping. She yawned and fell back into her, suddenly, very comfy pillow. As she closed her eyes, she vaguely heard Sebastian say, "…What about Jace? He's beginning to get worried about her…"

**A/N: Sorry, not very long, I know : ( But, I'm just not that good of an author right now, so, yeah… Review please!  
**


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